The Penguins of Madagascar: The Apocalypse Unfolds
by DrBlowhole1
Summary: It's been a while since the penguins have come across the evil Dr. Blowhole. Little do they know that he is coming up with a plan to end all plans. A plan that could change the whole country. The world. The universe. Rated T for blood, war, and language.
1. Ch 1: The Zoo Heist

**OK, so this is my first ever PoM fan fiction, so bare with me. ****I really wanted to write a story about Blowhole and the Penguins, so then I came up with this. I plan on making this the first of a series. Hopefully, this story doesn't fail. :)**

**THE PENGUINS OF MADAGASCAR: THE APOCALYPSE UNFOLDS**

_By: DarkLightEternal549_

**PART ONE: The Corrupt Campaign **

**"**_The Zoo Heist**"**_

**Location:**_ Central Park Zoo_

**Date:** _December_ _17, 2011; 10:47 P.M._

**Character:**_ Private  
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It was a cold, endless night in the streets of New York City as many citizens ran off to shop for Christmas presents. After all, Christmas was only in eight days.

No one happened to be visiting the Central Park Zoo; it was just too cold out! All of the animals just sat there in their habitats, waiting.

Then Alice walked out of her office, turning out the lights, closing the door, and clutching her keys. First she walked up to Boda and Bing, muttering to them something that only they could hear. Then she approached Marlene and did the same. In fact, she approached every animal in the zoo and repeated the process. All except for the Penguins.

Standing broadly outside of their lair were four sharp-looking penguins. On the left stood the short, young, feminine Private, who was freezing so hard that he was practically hugging himself. On the right stood the crazy maniac Rico, who was complaining about the cold to everyone else in his gibberish sort of way. Behind all of the penguins stood the very tall and intelligent Kowalski, who was busy trying to find a solution to when the zoo would close that night. And, finally, a brave, flat-headed Skipper stood in the front, commanding them to "just keep smiling and waving".

"Alright, listen up, penguins," said Alice as she approached their habitat with a look of annoyance on her face. "I'm closing up for the night. You little brats better not cause any trouble, do you hear me? Don't step out of those habitats, because I know you want to! The health department is coming in tomorrow to check on the habitats, and I don't want you screwing it up! So don't. Step. Out. Of that. Pin!"

The woman soon walked out of the zoo, locking the gate behind her.

"Well, S-ss-ss-kippah? What do we d-d-do now?" Asked Private as he shook away to chills.

"We go back into our stations, Private. A soldier never disobeys an order as important as that," explained Skipper. "Come on, boys."

Cheerfully to finally get back inside, the three penguins followed their leader into their underground lair. Kowalski settled by his working desk and began to pull out blueprints for a new invention. Rico sat down in the corner with his 'girlfriend'. Skipper walked over to the refrigerator at pulled out an iron mug and fish.

Private was the only one who didn't make a move to go do something of his liking. Instead, he walked up to Skipper. "Skippah?"

"Yes, Private?" Asked Skipper as he sipped on his mug.

"Do you think the cold will ever go away? I mean, this has to be the coldest winter ever," asked Private. "I think something might be wrong with the weather..."

"Kowalski? Options." Asked Skipper.

Kowalski lifted his head from the blueprints and pulled out a clipboard, immediately jotting down notes. "Either the sun is going out, the Earth has shifted drastically out of place, therefore discombobulating the climate and temperatures, or it is just a natural snow storm."

"See, young Private? There's nothing wrong here," said Skipper as he walked across the lair and reached his flipper into a cupboard. "Soldiers."

"Yes, Skipper?" Asked Kowalski, Rico, and Private as they stood in single-file line.

"Is anyone up for Operation: Double-dutch?" Asked Skipper as he held up a deck of cards for all of his men to see.

* * *

><p>Meanwhile, as the penguins set off playing cards, two, cloaked men were roaming around outside the zoo gate. "Are you sure this is going to work, Doug?" Asked the bigger man.<p>

"Shut up, Butch! Of course I'm sure! Now be quiet; I'm about to finish picking this lock..." Replied Doug as he grabbed hold of the lock on the gate and struck a needle into it.

Then it clicked.

"We're in," whispered Doug as he rushed off into the Central Park Zoo, Butch following in pursuit.

"Where's this Bali Mynah bird thing, Doug?" Asked Butch, tripping over his own two feet and quickly getting back.

"In the bird exhibit, knucklehead. Get up off your butt; you're going to alert the authorities!" Hissed Doug as he walked off down towards the bird house.

Butch nodded and followed his partner into the bird house.

"Peacock, parrot..." said Doug as he scanned the names of the birds. "Ah! Here it is: The Bali Mynah bird. Rarest of its species. We're gonna nab it, Butch."

"Where is it?" Asked Butch as he looked through the different habitats.

"Here..." Said Doug as he pointed at a small habitat in the back of the bird house. Within it perched a white bird with blue eyes and black wing tips. The Bali Mynah.

Doug stuck his hand in his pocket and withdrew a screwdriver. He handed it to Butch. "Unscrew the bolts, Butch. I'm going to go turn off the alarms..." And he left.

Butch gulped and held the screwdriver in his sweaty palm. Carefully, and quietly, he dug the tip into each bolt, removing each by hand. After five minutes, the window had been unscrewed.

It immediately collapsed to the ground, sending a surge of noise throughout the zoo.

Butch looked up and noticed the bird was watching him. With intent perseverance. "C-come here, pretty birdy!" He said as he gently raised his hand to snatch the Bali bird.

"Caw!" Cried the bird as it flew out of his grasp and toward the exit.

"N-n-no! Come back!" Cried Butch as he scrambled for the bird, only to fall smack down into the ground.

Butch looked up in horror, only to see his partner, Doug standing before him, clutching the crying bird by the leg.

"Shut up! You'll wake the whole neighborhood!" Hissed Doug.

"Sorry."

"Come on; we need to get disable the security cameras and destroy the footage," said Doug as he placed the bird in a small cage, handed it to Butch, and walked off toward the security office.

Butch sighed and carried the bird off toward the office.

* * *

><p>All four penguins halted at the sound of a loud boom.<p>

"What is it, Skippah?" Asked Private.

"I don't know, Private," said Skipper as he set his cards down. "Let's go, boys."

They all followed their leader out of their lair and out into the zoo.

Skipper stopped at the side of the security office. "Do you hear that, boys? Two voices... A fat man and a cunning crook!"

"What should we do, Skipper?" Asked Kowalski.

"Yeahghghh?" Asked Rico in his horrible, mispronouncing trademark.

"Is that a trick question, Kowalski? We fight!" Exclaimed Skipper. "Come on, boys."

Skipper and his followers busted down the door in one single kick. He flew through the air, kicking Butch to the ground. Kowalski and Private took on Doug, and Rico kept slapping Butch across the face.

"What the- Penguins?" Cried Doug as he smacked away Kowalski and Private. "Get them, Butch!"

"I'm trying!" Cried Butch as he attempted to stand up.

"Gah! Forget you!" Cried Doug as he snatched the cage from his overweight partner and fled out the building, running for a go cart just outside the office.

"Boys! Rico: Rope him!" Ordered Skipper.

Rico nodded, barfed up a rope, and tied the fat man.

All together, the four slid off down the path, catching up to the go cart extremely fast.

Doug looked in the side mirror, grasping the bird cage. "Blasted penguins!"

The go cart quickly swerved down the path, knocking down a light pole in the process.

But Skipper and the others had already gained up on the cart.

Rico threw himself up onto the hull of the cart, growling.

"Ah!" Cried Doug in disgust. Private popped up next to him, slapping him across the face.

Kowalski was busy writing down solutions to the problem.

Skipper pinned Doug to the chair, slapping him across the face multiple times.

Unable to see, and in physical pain, Doug lost control of the cart and crashed through several trees and light poles. The cart went flying through the gorilla habitat.

"No!" Cried Doug as he gained sight of the terrain ahead. Too late.

The cart went flying over a slope and through the sky, sending Doug flying out of the zoo in an non-logical sort of way. Strangely, he ended up crashing right into the back of a cop car.

The cage landed on the ground as well as Skipper and the others.

"Oh, thanks!" Said the Bali Mynah as he was released from the cage. "I owe you one."

"You don't have to owe us anything. It's all in the favor," said Skipper in a cocky sort of way.

"Oh, OK, then. Thanks anyway," said the bird as he flew back to his habitat.

Kowalski looked up from his clipboard. "Shall we go back to cards, Skipper?"

"You know the answer," said Skipper. "Job well done, boys. Job well done."

Private nodded and followed after his commander, Rico following behind. Kowalski was the last to leave.

"Smile and wave boys. Smile and wave..." Said Skipper as he disappeared into the following darkness.


	2. Ch 2: Inspection Day

**_The second chapter of the story as the Penguins face the consequences of their actions as the entire zoo suffers. _  
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**[Operation Acquired]  
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**"**_Inspection Day**"**_

**Location:**_ Central Park Zoo_

**Date:** _December 1__8, 2011; 9:30 A.M._

**Character:** _Skipper_

The alarm immediately rang throughout the lair as the morning wake-up call erupted.

"W-ah! Get back Mr. Gummy Fish! Don't make me use my slapping flippers on you!" Cried Skipper has he sprang into action and landed on the floor below, in signature fighting stance.

**"It's 9:30! It's 9:30! Wake up call! Wake up call! Get out of bed, you sleepyheads!" **Rang the voice of the lair.

Private sat up, rubbing his eyes. "Morning already?"

"Yeahghgha." Said Rico as he hopped down out of bed.

Kowalski sprang down the floor and immediately thrust out his clipboard.

"Kowalski, morning routine!" Ordered Skipper as he tidied himself up.

"First, we go out on our morning patrol around the zoo's interior and posterior. Then we advance in hardcore training and end the morning eating a fish or two, Skipper." Read Kowalski as he quickly put his clipboard away.

"Exactly. Men, move out!" Commanded Skipper as he lead his men out of the lair and habitat.

Noise could be heard all across the zoo.

"Quiet, soldiers!" Hissed Skipper as he put up a flipper to shush them.

"Oh, you're going to find that the zoo is very suitable for New York, Mr. Thompson. Here at the Central Park Zoo, we try our best to take care of the animals and make sure it is a pleasant stay for everyone," said Alice as she walked down the path with what appeared to be a stern, middle-aged man with partly-gray hair.

Mr. Thompson growled in annoyance. "Oh, shut up, would you? It is my decision whether or not this _playground _is suitable for New York. Now, please let me do my job!"

Alice opened her mouth as if to say something but stopped herself and nodded.

"Men, move on!" Whispered Skipper as he slid across the zoo after the two humans as they walked deeper into the zoo. His 'soldiers' followed after him.

"Here we have the bird inclosures," said Alice as she led Mr. Thompson into the birdhouse.

"Oh my God!" Cried Alice as she stopped in her tracks and immediately stepped in front of Mr. Thompson. "Oh, well that's it. Let's go show you the reptile house!"

Mr. Thompson growled. "What are you going on about?" He brushed past her and immediately growled with anger at the site of the broken inclosure and the partly-injured bird sitting inside.

"Please, Mr. Thompson. Let's please go back outside!" Said Alice.

Mr. Thompson grunted and walked outside in rage. Then he saw the road up ahead. Lamp posts and fences lay all over the path, leaves and destroyed bushes everywhere. The zoo was an absolute mess.

"Mr. Thompson, I promise! This wasn't like this when I left!" Protested Alice.

"And I suppose you left five years ago? Who's been running this piece of crap?" Questioned Mr. Thompson.

"Well, me. But you see..." Started Alice.

"Mhmm... I am afraid I am going now. Good luck, Miss Alice." Said Mr. Thompson as he jotted some notes on a clipboard and walked off down the destroyed path.

"No!" Screamed Alice as she sprang through the air and grabbed hold of his leg. "Please don't leave! I can pay you! This is the only job I have!"

They both turned their heads, for they were standing right by the security office. There in front of them was the fat, muscular Butch, whom had been tied up and lying there all night. "H-hi."

Mr. Thompson turned his head back to Alice and spat. "Good riddance, Miss Alice!" And he stormed off down to the zoo entrance.

"No! Don't go!" Cried Alice as she ran after Mr. Thompson.

But by then he was already outside the zoo gate. "Good day, Miss Alice!" He said for the final time as he threw his health note at her and slammed the gate, storming off toward his car.

The white parchment drifted through the air and landed splat on the ground. Alice picked it up and scanned through it, her eyes widening. In anger, she folded the slip and put it in her pocket, storming off toward the penguin habitat.

"Move, boys!" Cried Skipper as he flew off for the habitat, his comrades following at lightning speed. The four quickly stood in their signature stance within the habitat.

Alice reached the habitat and threw a fit. "Listen, penguins! You have messed with this zoo for the very last time! Do you know what you've done? Do ya?"

The penguins remained silent as Alice snarled and spat at the ground, tears practically raining down her face.

"Well you better be happy! You've ruined the community, the zoo, and, most importantly, MY LIFE!" Screamed Alice as she crumbled the health notification slip and threw it at the penguins. "So thanks..."

And she walked off.

"Skippah?" Asked Private. "Is it?"

Skipper picked up the slip and unfolded it, reading every last word of it. "Yes, Private. Yes..."

"Wha?" Asked Rico.

"Rico, it's best that you cover your ears. You wouldn't be able to stand the drama..." Explained Kowalski.

Rico shook his head. "Wha is iht?"

Skipper crumbled up the paper and threw it as far as possible. "Men. Fear the worst. At this point, our lives have changed dramatically. Expect the unexpected. We're on edge now... We let everyone down."

"Wha's happehnd?" Asked Rico, clearly not understanding.

Skipper frowned and down to the ground. "Rico, soldier, I don't know how to say this, but... the zoo has been shut down."


	3. Ch 3: Busy Planning

**The third chapter of the ever-going story as the Penguins begin to plan their next life.  
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**[Operation Acquired]  
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>"<strong>_Busy Planning**"**_

**Location:**_ Central Park Zoo_

**Date:** _December 1__8, 2011; 9:30 A.M._

**Character:** _Skipper_

"Wh- whah?" Rico cried as he slumped to the ground in a ball. He began to cry, rocking back and forth like a young child who had lost his toy.

Private, being the nicest and easiest to sadden, was very depressed from the idea. "How m-much time, Skippah?"

"7 A.M. tomorrow morning..." replied Skipper.

Kowalski immediately got to work on his clipboard. "That gives us approximately 21.5 hours to prepare before we are boarded off to the nearest zoo."

"What's the nearest zoo, Skippah?" Asked Private, holding his flippers in worry.

Skipper thought for a moment. When the answer came to his mind, his eyes widened. _Oh, shit! _

"Hoboken..." He scowled.

Everyone in the room became silent with anguish. Rico bawled even more than he was before. Private let out a few tears as well. Kowalski cocked his eyes in wonder.

"Are we really going to give up to Hoboken, Skipper?" He asked.

Skipper breathed deep. "No..." He growled, turning away from his recruits. "We'll find somewhere else to go..."

"But where, Skippah?" Asked Private.

Skipper pondered the question, banging his forehead with his flipper. "We'll go to Maine, make a new life in a new zoo... Our cover can't be blown..."

Private gasped and widened his eyes. "B-but what about the others! Burt, Julien, Marlene! All of them! What will happen to them?"

Skipper's face lit up at the sound of Marlene's name, but the expression soon abandoned his face without so much as a blush. "We'll go on without them. Leave them be, we'll meet new people over in Maine, no doubt about it! They'll learn to forget about us. It's too risky to bring them with us. One moment, we're in a zoo in Maine, the next we're on a cover magazine for the International Most-Wanted!"

Private let a few tears, backing up against the wall. He was just as saddened as Rico.

"Now, soldier, I don't want to see your sad face! You're going to be a man soon, and you need to act like one! You, too, Rico!" Ordered Skipper as he walked across the room to retreat to his quarters. "We'll leave at nightfall tonight..."

Private wiped away his tears and patted Rico on the back. "Don't worry, Rico..."

Rico payed to attention to him. He bawled again, and he cried some more... There was no stopping it...

Kowalski nodded. "Should we tell the others of the zoo's closing, Skipper?"

Skipper stopped halfway into his private quarters. "Negative, soldier."

Kowalski sighed and walked off into his laboratory to prepare for the voyage. He would need to pack all of his inventions, all of his latest hardware.

Private sniffled a bit, leaving the room to go pack his Lunacorn supply. "Get ready, Rico..."

Soon, the room grew silent. No one was left within in the room. All except Rico, who was crying his heart out.

* * *

><p><strong>Location: <strong>_Skipper's Quarters_

**Date:** _December 18, 2011; 9:35 A.M._

**Character:** _Skipper_

Skipper banged his head on his desk, knocking off a quill pen in the process. He was disturbed and horrified at the idea of having to leave the zoo behind. He had been here so long! Not to mention leaving behind Marlene...

A tear brushed down his face, which was very odd considering he never cries. Ever since he first met Marlene, he had loved her dearly. It didn't help that, whenever they worked together to stop something, it bonded them.

_Marlene, how I love you so! _Cried Skipper as he smacked his face in shame and looked at a picture of Marlene, which happened to be sitting within his desk drawer.

A tear abruptly stopped on the portrait.

Skipper put the picture into a box and placed it on his desk. Then he withdrew a tape recorder from deep within his drawer. He brought the device to his ear hole and pressed the play button firmly.

_"Skipper's log. 22:00 hours and no sign of any of my recruits waking. Today, I experienced a remarkable event. The zoo, as always, was in chaos. This time, the Rats were involved with the crime. Today was Marlene's first showing of love to me."_

_"I happened to save her life today. Just an instance away from being killed by the Rats' rolling blade, I managed to deactivite the blade with my very own face, taking the hurt of a thousand ways in the process. Marlene seemed all grateful for my saving of h__er life, and I hope we will grow together sooner enough. This is Skipper's log. Over and out."_

Skipper sighed, stopping the recording. He placed the tape recorder firmly within the box before sealing it tight with elastic tape. There was no chance Marlene was ever going to like him back. No chance. Especially now that he had to leave this way.

_Why now? _Screamed Skipper, tears brushing down his face. He slammed his forehead into his desk several times before he stopped. He was going to have a concussion if he didn't stop this nonsense. _Get a grip, Skipper! You'll find someone new..._

And, without a second thought, Skipper left the room, bolting the door behind him. All of the contents of the box within his quarters was all he would be taking with him. He was ready to leave. He just needed to wait out the day.

Skipper sighed, leaping out of the habitat to go finish out the day. If he even lived through it...

* * *

><p><strong>Location: <strong>_Unknown_

**Date: **_December 18, 10:00 A.M._

**Character: **_Axel_

Deep within a dark lair, a villain was constructing a diabolical plan to end all plans. It was the middle of the day, yet it seemed so dark.

Driving through a darkened hallway was the form of a vicious bottle-nosed dolphin with a hatred for penguins everywhere. The evil doctor smiled evily as he drove out onto a balcony high above New York City. He looked down upon the citizens walking through the streets with weery eyes, his bionic eye piece glowing red with anticipation. It didn't matter if they looked up here; he was far to high up to be seen.

"Soon, you humans will be mine to control. Mine to torture... Then we'll see who's the one jumping through hoops..." Growled Axel Blowhole, Skipper's arch-enemy.

A lobster approached Blowhole from behind, a clipboard in claw. "Dr. Blowhole!"

"Red One? What is it?" Scowled Blowhole as he turned around to look at his #1 lobster of his entire army.

"I just wanted to congratulate you on what you did back there at the Central Park Zoo. Using that new humanizer ray of yours to disguise yourself as a zoo health inspector? It was brilliant! That's the best thing I've seen from you yet, Dr. Blowhole!" Exclaimed Red One, moving his claws around to express his point.

"As usual, Red One. Thank you. Now get back to work," Ordered Blowhole as he turned to look back down at the humans.

"Yes, Dr. Blowhole," said Red One before leaving in a haste.

Blowhole sighed and looked back down at the humans. How annoying and weak they looked to him! It really made him mad...

Just then, a fellow bottle-nosed dolphin came up behind him, gently placing a flipper on his shoulder. "What's wrong, Blowy?"

Blowhole turned around to look at his beloved wife, Candy. He smiled, looking into her beautiful, ice blue eyes. Oh, how he loved her so much. "Hello, baby. I was just thinking about the humans... I kind of want to- nevermind..." He blushed.

"Do what?" Candy asked, wiping his brow with her flipper.

"This might sound childish, but I want to spit on one of them; like what they do on TV," explained Blowhole, blushing.

"Awh, Blowy..." Smiled Candy. "You should."

"Alright then..." Chuckled Blowhole as he leaned over the scaffolding and let loose a chunk of saliva. He watched as the spit landed on an unsuspecting man's head below. "Score!"

Candy giggled. "My evil genius."

Blowhole blushed, but it soon faded. He smiled and looked into Candy's eyes. Without a single hint of hesitation, he quickly pulled her into a kiss.

Candy's eyes lit up, returning the kiss. "Oh, Blowy..."

"Hehe," Chucked Blowhole, blushing a bit before licking her lips slightly. "I just felt like I had to do that."

"Oh..." Candy smiled, kissing back. Before she knew it, Blowhole had already slipped his tongue into her mouth, playing with her own tongue.

Blowhole grinned and licked her tongue and kissed her for a long moment. Candy kissed him back, moaning slightly. "Oh, Axel..."

Blowhole hugged her tightly and gazed into her eyes. "I love you, baby!"

Candy blushed. "I love you, too!"

Blowhole smiled and looked off into the horizon. "My plan is coming under way..."

"Speaking of plan," said Candy, kissing him. "You never told me what your plan was."

"Oh, you'll know soon enough. Trust me..." Said Blowhole, winking at her.

"Alright," Said Candy, hugging him tightly. "You're my evil genius..."

Blowhole hugged her back. "And you, my darling, are the love of my life."

The two both smiled and stayed hugging for minutes into hours.


End file.
